Dear Jae,

Alignment quality is definitely important and can have a strong effect on any of these evolutionary analysis. To my knowledge, the effect has not been analyzed extensively (either by us or by the developers of PAML and SLR) beyond pointing out that it is there and that evolutionary analyses on poor alignments cannot be trusted.

The bottom line is to always inspect alignments manually and be aware that any alignment errors may cause incorrect inference of phylogeny and/or selection.

Hope this helps,
Konrad